Open any biology textbook with decent evolution coverage, and you’ll find a version of a familiar diagram—a bat’s wing, a dolphin’s fin, a horse’s leg, a human’s arm. These vertebrate-limb structures are homologous, their similarities the result of shared origins in an ancestral mammal with a general-purpose limb. Evolution has modified each, but all have a common internal structure, a common embryological origin, and a fossil history that reveals a shared phylogenetic origin.

Comparative biology seems to make it clear that the limbs of invertebrates such as insects have different origins. There is little correspondence to what we see in our own structure: Insect limbs lack bones altogether. Embryologically, insect limbs arise as repeated segmental bulges in the cuticle. The comparative evolutionary history of vertebrates and invertebrates is most telling. The ancient chordate ancestors of our finned or limbed modern vertebrates were completely limbless, little more than undulating ribbons of eel-like swimmers, and our appendages are evolutionary novelties, less than 500 million years old. The arthropods, on the other hand, have been flourishing elaborate limbs for as long as they appear in the fossil record, beginning with tracks laid down in the pre-Cambrian, easily 500 million years ago. The last common ancestor of insects and mammals was a legless worm, and each of our lineages independently worked out how to build limbs, so they can’t be homologous.

The same can be said of other structures, like our eyes: The mirror eyes of scallops, the compound eyes of arthropods, and the camera eyes of chordates each represent a unique and unlinked solution to the problem of vision. We would not call a dragonfly eye and a human eye homologous—they seem so different, in so many ways, and the evidence suggests that our last common ancestor was eyeless, with little more than photosensitive spots.

And yet…

A curious phenomenon has nagged at biologists for the past few decades, as they have acquired better tools for probing deeper into the molecular biology of diverse organisms. Where they once assumed that the passage of vast amounts of time, over half a billion years in this case, would have produced divergences in the molecular patterns that govern animal forms as radical as those seen in the forms themselves, it now seems that something else transpired. As we discover more about the molecular basis of building structures like limbs and eyes, we’re finding more instances of homologous molecular players being recruited to do similar jobs in morphological features that are not themselves homologous.

Take insect and vertebrate limbs. They evolved independently, but the molecules that stake out the orientation and location of the various tissues within both kinds of limbs are homologous to an impressive degree. For example, a gene named distal-less in flies affects the tips of the limbs most strongly. A homologous mouse gene called Dlx, revealed as such by their nearly identical sequences, is similarly important in regulating the formation of the most distal elements of the limb.

The similarities go further. The dorsal-ventral boundaries of the vertebrate limb bud and the insect wing disc are established by a gene called fringe; other axes and boundaries are defined by genes in the wingless, apterous, hedgehog, and decapentaplegic families, and they operate in roughly similar ways in both groups of animals. This is like discovering that two cultures have independently invented a game like basketball, and then finding that while the games look vastly different in play, the court dimensions are the same, right down to the distance of the three-point line and the diameter of the center circle. It should make one question how independent their origins actually are.

The underlying similarities in eyes are even more striking. Eyes have evolved dozens of times and diverged wildly, as in the compound eyes of insects and the camera eyes of vertebrates, and have also on occasion converged on similar solutions. The octopus eye and the human eye superficially resemble each other from the outside, but structurally the tissues of each are organized in profoundly different ways, with different arrangements of cells in the retina, different kinds of photosensitive cells, and very different optic nerves. Dig deeper still, however, and all these eyes—octopus eyes, human eyes, fly eyes, spider eyes, flatworm eyespots—have a common master regulator gene, called Pax-6 in vertebrates and eyeless in flies. Wherever the animal expresses this gene, it initiates a cascade of activity that leads to the formation of an eye. And the genes are interchangeable! Extract Pax-6 from a mouse, inject it and express it in the limb of a fly, and the confused tissues of the fly will respond by assembling an eye—a fly’s eye—on its limb.

The photoreceptor types in the eyes were once thought to be distinct. Invertebrates have rhabodomeric cells that use a special version of the photopigment called r-opsin, and activate cells by a particular pathway called a phospholipase-C cascade. We vertebrates have ciliary cells, c-opsin, and a phosphodiesterase pathway. These are fundamental differences, and scientists have not changed their minds about the large differences between the two, but they have discovered an enlightening fact. Many animals have both! In our eyes, we primarily use the ciliary photoreceptors for vision, but we also maintain a set of rhabdomeric photoreceptors that have the job of sensing light to set circadian rhythms. Some invertebrates also have both, but they use the rhabdomeric receptors for vision and the ciliary receptors for circadian rhythms. It is not a difference in kind, but a difference in specialization and emphasis that distinguishes the visual systems of each lineage.

To make sense of the apparent conflict between anatomical divergence and a shared genetic inheritance, three biologists—Neil Shubin, Cliff Tabin, and Sean Carroll—have proposed that we need a new concept that they call deep homology. Evolution is a tinkerer that cobbles together new functions from old ones, and the genome is a kind of parts bin of recyclable elements. When new features evolve, the parts in the bin are co-opted to operate in new roles. As a result, the same parts appear in anatomically and evolutionarily distinct structures because it is faster and easier to reuse an old gene network that almost does what is needed, than it is to spend another few million years evolving a distinct gene for the function.

This makes these master genes precisely analogous to the stock of goods found in a hobbyist’s electronics store. Standard subunits—oscillators, op-amps, field effect transistors, switches, rheostats, and so forth—will get incorporated into many different kinds of projects; whether she is building a radio or a synthesizer or a burglar alarm, the hobbyist will find it easier to just grab an oscillator integrated circuit off the shelf than to design her own. We could sample devices built by different hobbyists with different purposes, and when we rummaged about in their insides, we would find the same subunits incorporated into novel, larger assemblies.

This is what we’re seeing in biology, too. We find an evolutionary novelty, like the vertebrate limb, and we can determine that it arose uniquely in our lineage. At the same time, we find a deeper heritage of shared genes that we hold in common with all other animals—a metazoan tool kit upon which we all draw to evolve.